Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report

Global Symmetry: Icosahedral - I  (3D View)
Global Stoichiometry: Homo 180-mer - A180 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content

• Total Structure Weight: 53.31 kDa 
• Atom Count: 3681 
• Modelled Residue Count: 417 
• Deposited Residue Count: 425 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

2IZ9

MS2-RNA HAIRPIN (4ONE -5) COMPLEX

• PDB DOI: 10.2210/pdb2IZ9/pdb
• Entry: 2IZ9 supersedes: 1DZS
• NDB: PR0258

• Classification: VIRUS/RNA
• Organism(s): Escherichia phage MS2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-07-25 Released: 2006-07-27 
• Deposition Author(s): Grahn, E., Stonehouse, N.J., Adams, C.J., Fridborg, K., Beigelman, L., Matulic-Adamic, J., Warriner, S.L., Stockley, P.G., Liljas, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Literature

Deletion of a Single Hydrogen Bonding Atom from the MS2 RNA Operator Leads to Dramatic Rearrangements at the RNA-Coat Protein Interface

Grahn, E., Stonehouse, N.J., Adams, C.J., Fridborg, K., Beigelman, L., Matulic-Adamic, J., Warriner, S.L., Stockley, P.G., Liljas, L.

(2000) Nucleic Acids Res 28: 4611

• PubMed: 11095669 
• DOI: 10.1093/nar/28.23.4611
• Primary Citation of Related Structures:  
  2IZ9


• PubMed Abstract: 
  

The MS2 coat protein binds specifically to an RNA hairpin formed within the viral genome. By soaking different RNA fragments into crystals of MS2 coat protein capsids it is possible to determine the X-ray structure of the RNA-protein complexes formed. Here we present the structure to 2.85 A resolution of a complex between a chemically modified RNA hairpin variant and the MS2 coat protein. This RNA variant has a substitution at the -5 base position, which has been shown previously to be pyrimidine-specific and is a uracil in the wild-type RNA. The modified RNA hairpin contains a pyridin-4-one base (4one) at this position that lacks the exocyclic 2-oxygen eliminating the possibility of forming a hydrogen bond to asparagine A87 in the protein. The 4one complex structure shows an unprecedented major conformational change in the loop region of the RNA, whereas there is almost no change in the conformation of the protein.

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Organizational Affiliation: 

Department of Cell and Molecular Biology, Uppsala University, Box 596, SE-751 24 Uppsala, Sweden.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MS2 COAT PROTEIN	A, B, C	129	Escherichia phage MS2	Mutation(s): 0
UniProt
Find proteins for P03612 (Escherichia phage MS2) Explore P03612  Go to UniProtKB:  P03612

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*U ONEP *AP*CP*CP*CP*AP*UP*GP*U)-3'	D [auth R], E [auth S]	19	Escherichia phage MS2

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 0.220 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 288	α = 90
b = 288	β = 90
c = 653	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-07-25 
• Released Date: 2006-07-27 
Deposition Author(s): Grahn, E., Stonehouse, N.J., Adams, C.J., Fridborg, K., Beigelman, L., Matulic-Adamic, J., Warriner, S.L., Stockley, P.G., Liljas, L.
• This entry supersedes: 1DZS

Revision History  

• Version 1.0: 2006-07-27
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection